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about the subarray


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#1 fzhang

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Posted 22 November 2009 - 05:42 AM

hi, everyone, I am a novice in the field of microarray and I have some questions.

My research object is a bacteria with about 2000 ORFs in total. And I found that many microarray manufacturers have different formats of dna chip. And some of these chips have many subarrays. Agilent for example, has chips in a 8 x 15K format.

I don't know much why we need to print as many as 8 identical subarrays on one carrier. Is this simply a technical duplication?

And I am going to study the expression profile of my bacteria under 2 different temperatures. And if I am going to use this 8 x 15K chip, I will have 8 duplications, right? Is it a great waste?

I am really puzzled at this. And thanks in advance!

#2 gogreen

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Posted 23 November 2009 - 05:55 AM

Hi fzhang,

The Aglient's 8X15k means 8 identical arrays on 1 slide as you said...but doesn't mean you have to do technical replicates for the same sample on all the 8. You can actually hybridize 8 different samples which you can decide based on your interests..
Agilent offers 4 array formats..which are 1 array/slide, 2 arrays/slide, 4 arrays/slide, 8 arrays/slide..The number of probes printed varies from 244k, 105k, 44k and 15k respectively. The newer high density arrays are a million spots for the single array, 400k for 2 array/slide and so on.

You can process 8 samples on a single slide with 1 control and 7 time references (for eg.!) with 1 color expt or 16 samples (ideally control vs treated) which can be different controls for different treated samples allowing you to compare 8 different experiments in 1 slide with a dual color expt! Also since the ararys are on same slide, the variations in the washing can be greatly reduced too.

Hope this helps

gogreen

Edited by gogreen, 23 November 2009 - 05:56 AM.





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